Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate PfGW456L13_1920 Histidine transporter, periplasmic histidine-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09620 (322 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1920 Length = 337 Score = 327 bits (839), Expect = 2e-94 Identities = 164/343 (47%), Positives = 233/343 (67%), Gaps = 27/343 (7%) Query: 1 MKSNKTLL-TTLLSMGLLAS-AGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEK 58 M+S KTLL ++LL++ LL+ A AT+ A P+ F + WESG L+T++L++++EK Sbjct: 1 MRSIKTLLGSSLLALSLLSHPASATEKAA------PIHFGDITWESGSLITEILRLIVEK 54 Query: 59 GYDCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIE 118 GY TD+LPG+++++E AL+ NDIQV EEW GRS W KA GKV G+G V GA E Sbjct: 55 GYGYPTDTLPGSTVSLEAALAKNDIQVIGEEWAGRSPAWVKAAAEGKVFGLGDTVKGATE 114 Query: 119 GWYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELD 178 GW+VP YV++GD +R ++ AP LK++ADL +Y VF+DPE+PS+GRF N P GWT E+ Sbjct: 115 GWWVPEYVIKGDPERGIKPLAPELKSVADLAKYKDVFRDPEDPSRGRFLNSPTGWTSEIV 174 Query: 179 NSEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEE 238 NS+ LK+Y L +Y NFR G+G ALDA V SS +RG+P+LFYYWSPTPL+G+ LVKL+E Sbjct: 175 NSQKLKAYDLTASYVNFRTGSGAALDAEVASSIRRGKPVLFYYWSPTPLLGRFKLVKLDE 234 Query: 239 KPGVDKS-------------------VSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQ 279 P ++ S+ +G+S F + P+LV EKV+LPID+LNQ Sbjct: 235 PPFDAEAWKTLADANNPNPKGTRSMPASLAIGVSAPFKAQYPDLVTFFEKVDLPIDLLNQ 294 Query: 280 NLGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDAAKKIDAAL 322 LG+M+++R + ++A+ FL+E P+VW WV + A K+ A+L Sbjct: 295 TLGQMSEKRQKPREVAEAFLREQPQVWKGWVPGEVATKVSASL 337 Lambda K H 0.314 0.133 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 339 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 322 Length of database: 337 Length adjustment: 28 Effective length of query: 294 Effective length of database: 309 Effective search space: 90846 Effective search space used: 90846 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory